Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Nat Genet. 2020 Oct;52(10):991-998. doi: 10.1038/s41588-020-0700-8.
: Researchers are generating molecular data pertaining to the SARS-CoV-2 RNA genome and its proteins at an unprecedented rate during the COVID-19 pandemic. As a result, there is a critical need for rapid and continuously updated access to the latest molecular data in a format in which all data can be quickly cross-referenced and compared. We adapted our genome browser visualization tool to the viral genome for this purpose. Molecular data, curated from published studies or from database submissions, are mapped to the viral genome and grouped together into “annotation tracks” where they can be visualized along the linear map of the viral genome sequence and programmatically downloaded in standard format for analysis.
: The UCSC Genome Browser for SARS-CoV-2 (https://genome.ucsc.edu/covid19.html) provides continuously updated access to the mutations in the many thousands of SARS-CoV-2 genomes deposited in GISAID and the international nucleotide sequencing databases, displayed alongside phylogenetic trees. These data are augmented with alignments of bat, pangolin, and other animal and human coronavirus genomes, including per-base evolutionary rate analysis. All available annotations are cross-referenced on the virus genome, including those from major databases (PDB, RFAM, IEDB, UniProt) as well as up-to-date individual results from preprints. Annotated data include predicted and validated immune epitopes, promising antibodies, RT-PCR and sequencing primers, CRISPR guides (from research, diagnostics, vaccines, and therapies), and points of interaction between human and viral genes. As a community resource, any user can add manual annotations which are quality checked and shared publicly on the browser the next day.
: We invite all investigators to contribute additional data and annotations to this resource to accelerate research and development activities globally. Contact us at genome-www@soe.ucsc.edu with data suggestions or requests for support for adding data. Rapid sharing of data will accelerate SARS-CoV-2 research, especially when researchers take time to integrate their data with those from other labs on a widely-used community browser platform with standardized machine-readable data formats, such as the SARS-CoV-2 Genome Browser.
在 COVID-19 大流行期间，研究人员正在以前所未有的速度生成与 SARS-CoV-2 RNA 基因组及其蛋白质相关的分子数据。因此，迫切需要以一种可以快速交叉引用和比较所有数据的格式，快速且持续地获取最新的分子数据。为此，我们针对病毒基因组对我们的基因组浏览器可视化工具进行了适配。从已发表的研究或从数据库提交中提取的分子数据被映射到病毒基因组上，并被分为“注释轨道”，在这些轨道中，它们可以沿着病毒基因组序列的线性图谱进行可视化，并以标准格式进行编程下载以进行分析。
UCSC SARS-CoV-2 基因组浏览器（https://genome.ucsc.edu/covid19.html）提供了对 GISAID 和国际核苷酸测序数据库中数千个 SARS-CoV-2 基因组中突变的持续更新访问，同时还显示了系统发育树。这些数据与蝙蝠、穿山甲和其他动物及人类冠状病毒基因组的比对结果一起被扩充，包括基于碱基的进化率分析。病毒基因组上交叉引用了所有可用的注释，包括来自主要数据库（PDB、RFAM、IEDB、UniProt）的注释，以及来自预印本的最新的个别结果。注释数据包括预测和验证的免疫表位、有前途的抗体、RT-PCR 和测序引物、CRISPR 向导（来自研究、诊断、疫苗和疗法）以及人类和病毒基因之间的相互作用点。作为一个社区资源，任何用户都可以添加手动注释，这些注释将经过质量检查，并在第二天在浏览器上公开共享。
我们邀请所有研究人员为该资源添加额外的数据和注释，以加速全球的研究和开发活动。有数据建议或需要支持添加数据，请发送电子邮件至 genome-www@soe.ucsc.edu 与我们联系。快速共享数据将加速 SARS-CoV-2 的研究，特别是当研究人员花时间将他们的数据与其他实验室的数据整合到一个广泛使用的具有标准化机器可读数据格式的社区浏览器平台（如 SARS-CoV-2 基因组浏览器）上时。
